Fix: Adding Pace and PySHiELD unit tests back in to workflow

.github/workflows/gh_pages_doc.yml

@@ -26,7 +26,7 @@ jobs:
           git config user.email github-actions[bot]@users.noreply.github.com
       - uses: actions/setup-python@v5
         with:
-            python-version: 3.x
+          python-version: 3.x
       - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
       - uses: actions/cache@v4
         with:

.github/workflows/lint.yaml

@@ -6,21 +6,21 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-        - name: Checkout repository
-          uses: actions/checkout@v4
+      - name: Checkout repository
+        uses: actions/checkout@v4
 
-        - name: Setup Python 3.11
-          uses: actions/setup-python@v5
-          with:
-            python-version: '3.11'
+      - name: Setup Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
 
-        - name: Install pre-commit
-          run: |
-            pip install pre-commit
-        - name: Run lint via pre-commit
-          run: |
-            pre-commit run --all-files
+      - name: Install pre-commit
+        run: |
+          pip install pre-commit
+      - name: Run lint via pre-commit
+        run: |
+          pre-commit run --all-files
 
-        - name: Check advection code consistency
-          run: |
-            ./.github/workflows/scripts/ensure_xppm_yppm_consistency.sh
+      - name: Check advection code consistency
+        run: |
+          ./.github/workflows/scripts/ensure_xppm_yppm_consistency.sh

.github/workflows/pace_tests.yaml

@@ -1,15 +1,10 @@
-# TODO: Re-activate after PR 60
-# TODO: Temporarily removing tests due to dependent changes in
-#       Pace#129, PyFV3#64 PRs; tests should be reverted back after
-#       these PRs are merged.
+name: "pace main tests"
+on:
+  pull_request:
 
-# name: "pace main tests"
-# on:
-#   pull_request:
-
-# jobs:
-#   pace_main_tests:
-#     uses: NOAA-GFDL/pace/.github/workflows/main_unit_tests.yaml@develop
-#     with:
-#       component_trigger: true
-#       component_name: pyFV3
+jobs:
+  pace_main_tests:
+    uses: NOAA-GFDL/pace/.github/workflows/main_unit_tests.yaml@develop
+    with:
+      component_trigger: true
+      component_name: pyFV3

.github/workflows/pyshield_tests.yaml

@@ -1,11 +1,10 @@
-# TODO: Reactivate after PR 60
-# name: "pySHiELD translate tests"
-# on:
-#   pull_request:
+name: "pySHiELD translate tests"
+on:
+  pull_request:
 
-# jobs:
-#   pyshield_translate_tests:
-#     uses:  NOAA-GFDL/PySHiELD/.github/workflows/translate.yaml@develop
-#     with:
-#       component_trigger: true
-#       component_name: pyFV3
+jobs:
+  pyshield_translate_tests:
+    uses: NOAA-GFDL/PySHiELD/.github/workflows/translate.yaml@develop
+    with:
+      component_trigger: true
+      component_name: pyFV3

.github/workflows/translate.yaml

@@ -32,7 +32,7 @@ jobs:
         uses: actions/checkout@v4
         with:
           submodules: 'recursive'
-          repository:  noaa-gfdl/pyFV3
+          repository: noaa-gfdl/pyFV3
           path: pyFV3
 
       - name: Checkout hash that triggered CI
@@ -43,14 +43,14 @@ jobs:
 
       - name: External trigger install NDSL packages
         if: ${{inputs.component_trigger}}
-        run:  |
+        run: |
           cd ${GITHUB_WORKSPACE}/pyFV3
           cd NDSL && pip3 install .[test] && cd ../
           pip3 install .[test]
 
       - name: Install pyFV3 packages
         if: ${{ ! inputs.component_trigger }}
-        run : |
+        run: |
           cd ${GITHUB_WORKSPACE}/pyFV3
           pip install .[ndsl,test]
 
@@ -73,7 +73,7 @@ jobs:
       - name: NumPy FvTp2d
         run: |
           cd ${GITHUB_WORKSPACE}/pyFV3
-          coverage run --rcfile=setup.cfg -m pytest \
+          coverage run --rcfile=pyproject.toml -m pytest \
               -v -s --data_path=${{ env.DATA_PATH }} \
               --backend=numpy \
               --which_modules=FvTp2d \
@@ -82,18 +82,18 @@ jobs:
 
       - name: Numpy D_SW
         run: |
-         cd ${GITHUB_WORKSPACE}/pyFV3
-         coverage run --rcfile=setup.cfg -m pytest \
-              -v -s --data_path=${{ env.DATA_PATH }} \
-              --backend=numpy \
-              --which_modules=D_SW \
-              --threshold_overrides_file=./tests/savepoint/translate/overrides/standard.yaml \
-              ./tests/savepoint
+          cd ${GITHUB_WORKSPACE}/pyFV3
+          coverage run --rcfile=pyproject.toml -m pytest \
+               -v -s --data_path=${{ env.DATA_PATH }} \
+               --backend=numpy \
+               --which_modules=D_SW \
+               --threshold_overrides_file=./tests/savepoint/translate/overrides/standard.yaml \
+               ./tests/savepoint
 
       - name: Numpy Remapping
         run: |
           cd ${GITHUB_WORKSPACE}/pyFV3
-          coverage run --rcfile=setup.cfg -m pytest \
+          coverage run --rcfile=pyproject.toml -m pytest \
               -v -s --data_path=${{ env.DATA_PATH }} \
               --backend=numpy \
               --which_modules=Remapping \
@@ -107,7 +107,7 @@ jobs:
           export PACE_FLOAT_PRECISION=64
           export OMP_NUM_THREADS=1
           export PACE_LOGLEVEL=Debug
-          mpiexec -mca orte_abort_on_non_zero_status 1 -np 6 --oversubscribe coverage run --rcfile=setup.cfg -m mpi4py -m pytest \
+          mpiexec -mca orte_abort_on_non_zero_status 1 -np 6 --oversubscribe coverage run --rcfile=pyproject.toml -m mpi4py -m pytest \
             -v -s --data_path=${{ env.DATA_PATH }} \
             --backend=dace:cpu \
             -m parallel \

.pre-commit-config.yaml

@@ -2,51 +2,43 @@ default_language_version:
   python: python3
 
 repos:
--   repo: https://github.com/psf/black
+  - repo: https://github.com/psf/black
     rev: 25.1.0
     hooks:
-    - id: black
-      additional_dependencies: ["click==8.0.4"]
+      - id: black
 
--   repo: https://github.com/pre-commit/mirrors-isort
+  - repo: https://github.com/pre-commit/mirrors-isort
     rev: v5.10.1
     hooks:
-    - id: isort
-      args: ["--profile", "black"]
+      - id: isort
+        args: ["--profile", "black"]
 
--   repo: https://github.com/pre-commit/mirrors-mypy
+  - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.17.0
     hooks:
-    - id: mypy
-      name: mypy-fv3core
-      args: [--config-file, setup.cfg]
-      additional_dependencies: [types-PyYAML]
-      files: pyFV3
-      exclude: |
-        (?x)^(
-        pyFV3/stencils/fv_subgridz.py |
-        pyFV3/tests/conftest.py
-        )$
--   repo: https://github.com/pre-commit/pre-commit-hooks
+      - id: mypy
+        name: mypy-fv3core
+        args: [--config-file, pyproject.toml]
+        files: pyFV3
+  - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
-    - id: check-toml
-    - id: check-yaml
-    - id: end-of-file-fixer
-    - id: trailing-whitespace
--   repo: https://github.com/pycqa/flake8
+      - id: check-toml
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/pycqa/flake8
     rev: 7.3.0
     hooks:
-    - id: flake8
-      name: flake8
-      language_version: python3
-      args: [--config, setup.cfg]
-      exclude: |
-        (?x)^(
-        .*/__init__.py |
-        )$
-    - id: flake8
-      name: flake8 __init__.py files
-      files: "__init__.py"
-      # ignore unused import error in __init__.py files
-      args: ["--ignore=F401,E203", --config, setup.cfg]
+      - id: flake8
+        name: flake8
+        language_version: python3
+        additional_dependencies: [Flake8-pyproject]
+
+  - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+    rev: v2.15.0
+    hooks:
+      - id: pretty-format-toml
+        args: [--autofix, --indent, "2"]
+      - id: pretty-format-yaml
+        args: [--autofix, --preserve-quotes, --indent, "2", --offset, "2"]

mkdocs.yml

@@ -15,47 +15,47 @@ plugins:
 nav:
   - Home: index.md
   - Top:
-    - "_config": top/_config.md
-    - "dycore_state": top/dycore_state.md
-    - "version": top/version.md
+      - "_config": top/_config.md
+      - "dycore_state": top/dycore_state.md
+      - "version": top/version.md
   - Stencils:
-    - "a2b_ord4": stencils/a2b_ord4.md
-    - "c_sw": stencils/c_sw.md
-    - "d2a2c_vect": stencils/d2a2c_vect.md
-    - "d_sw": stencils/d_sw.md
-    - "del2cubed": stencils/del2cubed.md
-    - "delnflux": stencils/delnflux.md
-    - "divergence_damping": stencils/divergence_damping.md
-    - "dyn_core": stencils/dyn_core.md
-    - "fillz": stencils/fillz.md
-    - "fv_dynamics": stencils/fv_dynamics.md
-    - "fv_subgridz": stencils/fv_subgridz.md
-    - "fvtp2d": stencils/fvtp2d.md
-    - "fxadv": stencils/fxadv.md
-    - "map_single": stencils/map_single.md
-    - "mapn_tracer": stencils/mapn_tracer.md
-    - "moist_cv": stencils/moist_cv.md
-    - "neg_adj3": stencils/neg_adj3.md
-    - "nh_p_grad": stencils/nh_p_grad.md
-    - "pe_halo": stencils/pe_halo.md
-    - "pk3_halo": stencils/pk3_halo.md
-    - "ppm": stencils/ppm.md
-    - "ray_fast": stencils/ray_fast.md
-    - "remap_profile": stencils/remap_profile.md
-    - "remapping": stencils/remapping.md
-    - "riem_solver3": stencils/riem_solver3.md
-    - "riem_solver_c": stencils/riem_solver_c.md
-    - "saturation_adjustment": stencils/saturation_adjustment.md
-    - "sim1_solver": stencils/sim1_solver.md
-    - "temperature_adjust": stencils/temperature_adjust.md
-    - "tracer_2d_1l": stencils/tracer_2d_1l.md
-    - "updatedzc": stencils/updatedzc.md
-    - "updatedzd": stencils/updatedzd.md
-    - "xppm": stencils/xppm.md
-    - "xtp_u": stencils/xtp_u.md
-    - "yppm": stencils/yppm.md
-    - "ytp_v": stencils/ytp_v.md
+      - "a2b_ord4": stencils/a2b_ord4.md
+      - "c_sw": stencils/c_sw.md
+      - "d2a2c_vect": stencils/d2a2c_vect.md
+      - "d_sw": stencils/d_sw.md
+      - "del2cubed": stencils/del2cubed.md
+      - "delnflux": stencils/delnflux.md
+      - "divergence_damping": stencils/divergence_damping.md
+      - "dyn_core": stencils/dyn_core.md
+      - "fillz": stencils/fillz.md
+      - "fv_dynamics": stencils/fv_dynamics.md
+      - "fv_subgridz": stencils/fv_subgridz.md
+      - "fvtp2d": stencils/fvtp2d.md
+      - "fxadv": stencils/fxadv.md
+      - "map_single": stencils/map_single.md
+      - "mapn_tracer": stencils/mapn_tracer.md
+      - "moist_cv": stencils/moist_cv.md
+      - "neg_adj3": stencils/neg_adj3.md
+      - "nh_p_grad": stencils/nh_p_grad.md
+      - "pe_halo": stencils/pe_halo.md
+      - "pk3_halo": stencils/pk3_halo.md
+      - "ppm": stencils/ppm.md
+      - "ray_fast": stencils/ray_fast.md
+      - "remap_profile": stencils/remap_profile.md
+      - "remapping": stencils/remapping.md
+      - "riem_solver3": stencils/riem_solver3.md
+      - "riem_solver_c": stencils/riem_solver_c.md
+      - "saturation_adjustment": stencils/saturation_adjustment.md
+      - "sim1_solver": stencils/sim1_solver.md
+      - "temperature_adjust": stencils/temperature_adjust.md
+      - "tracer_2d_1l": stencils/tracer_2d_1l.md
+      - "updatedzc": stencils/updatedzc.md
+      - "updatedzd": stencils/updatedzd.md
+      - "xppm": stencils/xppm.md
+      - "xtp_u": stencils/xtp_u.md
+      - "yppm": stencils/yppm.md
+      - "ytp_v": stencils/ytp_v.md
   - Utils:
-    - "functional_validation": utils/functional_validation.md
+      - "functional_validation": utils/functional_validation.md
   - Wrappers:
-    - "geos_wrapper": wrappers/geos_wrapper.md
+      - "geos_wrapper": wrappers/geos_wrapper.md

pyfv3/__init__.py

@@ -9,3 +9,10 @@
 DryConvectiveAdjustment: Sub-grid dry convective adjustment
 DynamicalCore: The FV3 dynamical core
 """
+
+__all__ = [
+    "DynamicalCoreConfig",
+    "DycoreState",
+    "DryConvectiveAdjustment",
+    "DynamicalCore",
+]

pyfv3/initialization/__init__.py

@@ -4,3 +4,5 @@
 """
 init_analytic_state: Creates dycore state object out of analytic initial conditions
 """
+
+__all__ = ["init_analytic_state"]

pyfv3/stencils/__init__.py

@@ -63,3 +63,37 @@
 XPiecewiseParabolic: Piecewise parabolic method advection in x-direction
 YPiecewiseParabolic: Piecewise parabolic method advection in y-direction
 """
+
+__all__ = [
+    "AGrid2BGridFourthOrder",
+    "CGridShallowWaterDynamics",
+    "DGrid2AGrid2CGridVectors",
+    "DGridShallowWaterLagrangianDynamics",
+    "HyperdiffusionDamping",
+    "DelnFlux",
+    "DelnFluxNoSG",
+    "DivergenceDamping",
+    "AcousticDynamics",
+    "FillNegativeTracerValues",
+    "DynamicalCore",
+    "DryConvectiveAdjustment",
+    "FiniteVolumeTransport",
+    "FiniteVolumeFluxPrep",
+    "MapSingle",
+    "MapNTracer",
+    "AdjustNegativeTracerMixingRatio",
+    "NonHydrostaticPressureGradient",
+    "PK3Halo",
+    "RayleighDamping",
+    "RemapProfile",
+    "LagrangianToEulerian",
+    "NonhydrostaticVerticalSolver",
+    "NonhydrostaticVerticalSolverCGrid",
+    "SatAdjust3d",
+    "Sim1Solver",
+    "TracerAdvection",
+    "UpdateGeopotentialHeightOnCGrid",
+    "UpdateHeightOnDGrid",
+    "XPiecewiseParabolic",
+    "YPiecewiseParabolic",
+]